8Y9S | pdb_00008y9s

Crystal structure of nanobody MY6321 bound to human serum albumin (HSA)

• PDB DOI: https://doi.org/10.2210/pdb8Y9S/pdb

• Classification: PROTEIN BINDING
• Organism(s): Homo sapiens, Vicugna pacos
• Expression System: Oryza sativa, Saccharomyces cerevisiae
• Mutation(s): No 


• Deposited: 2024-02-07 Released: 2025-02-12 
• Deposition Author(s): Ding, Y., Zhong, P.Y.
• Funding Organization(s): National Science Foundation (NSF, China), Ministry of Science and Technology (MoST, China)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.88 Å
• R-Value Free: 
  0.293 (Depositor), 0.306 (DCC) 
• R-Value Work: 
  0.230 (Depositor), 0.253 (DCC) 
• R-Value Observed: 
  0.233 (Depositor) 

Starting Models: experimental

Literature

Crystal structure of nanobody MY6321 bound to human serum albumin (HSA)

Ding, Y., Zhong, P.Y.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: gel filtration, isothermal titration calorimetry, surface plasmon resonance

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 160.97 kDa 
• Atom Count: 10,913 
• Modeled Residue Count: 1,382 
• Deposited Residue Count: 1,426 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Albumin	A, C	591	Homo sapiens	Mutation(s): 0  Gene Names: ALB
UniProt & NIH Common Fund Data Resources
Find proteins for P02768 (Homo sapiens) Explore P02768  Go to UniProtKB:  P02768
PHAROS:  P02768 GTEx:  ENSG00000163631

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
nanobody MY6321	B, D	122	Vicugna pacos	Mutation(s): 0

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.88 Å
• R-Value Free:  0.293 (Depositor), 0.306 (DCC) 
• R-Value Work:  0.230 (Depositor), 0.253 (DCC) 
• R-Value Observed: 0.233 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 65.26	α = 90
b = 143.9	β = 100.23
c = 93.67	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data scaling
XDS	data reduction
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-02-12 
Deposition Author(s): Ding, Y., Zhong, P.Y.

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Funding Organization	Location	Grant Number
National Science Foundation (NSF, China)	China	32070939
National Science Foundation (NSF, China)	China	82030106
Ministry of Science and Technology (MoST, China)	China	2021YFA0805200

Revision History  

• Version 1.0: 2025-02-12
  Type: Initial release
  
• Version 1.1: 2025-02-26
  Changes: Derived calculations